In the menu that comes up when you press Esc in-game there are 'stains' along the bottom of the screen and behind the menu entries. Can this be disabled somehow (for a mod) by modifying a file? Or is it a hard coded effect?

Hmmm, I think they're hard coded, but I'd have to ask Edmundo who did the menus. Anyways, a possible fix would be to locate those images and change them fore something you like more or change them for a transparent shader so you don't see them at all.